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- PDB-6oti: Carbonic Anhydrase IX mimic complexed with ureic benzene sulfonam... -

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Basic information

Entry
Database: PDB / ID: 6oti
TitleCarbonic Anhydrase IX mimic complexed with ureic benzene sulfonamide MB9-561B
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / ureido benzene sulfonamide / carbonic anhydrase / inhibitor / LYASE / lyase-lyase inhibitor complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Chem-N84 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKota, A. / McKenna, R.
CitationJournal: To Be Published
Title: Carbonic Anhydrase IX mimic complexed with ureido benzene sulfonamide MB9-561B
Authors: Kota, A. / McKenna, R.
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3544
Polymers28,8441
Non-polymers5103
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.503, 41.603, 72.490
Angle α, β, γ (deg.)90.000, 103.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-N84 / 4-hydroxy-3-({[(pyridin-4-yl)methyl]carbamoyl}amino)benzene-1-sulfonamide


Mass: 322.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris-HCL, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.86 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 2→29.323 Å / Num. obs: 16030 / % possible obs: 94.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.64
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.33 / Num. unique obs: 1625

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 2→29.323 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.18
RfactorNum. reflection% reflection
Rfree0.2543 793 4.98 %
Rwork0.199 --
obs0.2019 15937 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.41 Å2 / Biso mean: 27.3923 Å2 / Biso min: 4.36 Å2
Refinement stepCycle: final / Resolution: 2→29.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 31 36 2109
Biso mean--40.73 26.26 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.12540.34021300.26772566269696
2.1254-2.28950.31881180.26432412253092
2.2895-2.51980.33281360.24272536267295
2.5198-2.88410.24841320.222514264694
2.8841-3.63260.24811360.17782569270596
3.6326-29.32650.19931410.15382547268893
Refinement TLS params.Method: refined / Origin x: -30.4337 Å / Origin y: -1.3699 Å / Origin z: 16.1508 Å
111213212223313233
T0.0405 Å20.0047 Å20.0025 Å2-0.0394 Å20.0058 Å2--0.0435 Å2
L0.6763 °20.0283 °20.0032 °2-0.7322 °20.2101 °2--0.718 °2
S-0.0123 Å °-0.0205 Å °0.0412 Å °-0.0434 Å °0.0262 Å °-0.0442 Å °-0.0084 Å °-0.0076 Å °0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 41
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allE1

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